Nautilus was first released in 2001 and development has continued ever since. The following is a brief timeline of its development history:

Version 1.0 was released on March 13, 2001,[5] and incorporated into GNOME 1.4.[6]

Version 2.0 was a port to GTK+ 2.0.

Version 2.2 included changes to make it more compliant with User Interface Guidelines.

Version 2.4 switched the desktop folder to ~/Desktop (the ~ represents the user's "Home" folder) to be compliant with freedesktop.org standards.

In the version included with GNOME 2.6, Nautilus switched to a spatial interface.[7] The "classic" interface is still available by a filing cabinet shaped icon, by an option in the "Edit -> Preferences -> Behavior" menu in Nautilus, in a folder's context menu, and by using the "--browser" switch when started by a command via a launcher or shell. Several Linux distributions have made "browser" mode the default.

GNOME 2.14 introduced a version of Nautilus with improved searching, integrated optional Beagle support and the ability to save searches as virtual folders.[8][9]

With the release of GNOME 2.22, Nautilus was ported to the newly introduced GVfs, the replacement virtual file system for the aging GnomeVFS.

The 2.32 release introduced a dialog for handling conflicts when performing copy or move operation, transparency icon effect when cutting files into folder and enhanced the Wastebucket with Restore files.[11] Besides, this is the last version that is based on GTK2 before the move to GNOME 3.0 with GTK3.

GNOME 3.0 completely revamped the UX of Nautilus with focus on neat and elegant element like the sidebar and icons. Additionally, the Connect to Server dialog is also enhanced.[12] Nautilus was ported to GTK3.

Version 3.6 introduced a revamped UI design, symbolic sidebar icon, new search feature, removal of many features such as setting window background, emblems, split pane mode, spatial mode, scripts, compact view mode and tree view. Nautilus' application name was renamed to Files, Though it is still called Nautilus internally in some distributions.[14] These major changes led to a lot of criticism, and various vendors such as Linux Mint decided to fork version 3.4.[15][16]

Bookmarks, window backgrounds, notes, and add-on scripts are all implemented, and the user has the choice between icon, list, or compact list views. In browser mode, Nautilus keeps a history of visited folders, similar to web browsers, permitting quick revisiting of folders.

Nautilus can display previews of files in their icons, be they text files, images, sound or video files via thumbnailers such as Totem. Audio files are previewed (played back over GStreamer) when the pointer is hovering over them.

Using the GIO library, Nautilus tracks modification of local files in real time, eliminating the need to refresh the display. GIO internally supports Gamin and FAM, Linux' inotify and Solaris' File Events Notification system.

MIME types (also called "media type" or "content type") are standardized by the IANA, then the freedesktop.org project takes care that the implementation works across all free software desktops. shared-mime-info is the provided library.[23] At this time, at least GNOME, KDE, Xfce and ROX use this database.